[gmx-users] Increase temperature to 550K

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> The system = one lysozyme + TIP3P water
> I was put the system in NTP simulation.
> 
> Under 550K, all water molecules should evaporate entirely , I suppose ???
> 

Is this what you want to happen?  Are the force field parameters appropriate for 
such behavior?

> 
>>From Justin =>
> "There are plenty of other methodological concerns (pressure
> coupling especially) "
> Would you please direct me about this ?
> 

Yes, search the literature.  As I said, a number of groups have been doing 
high-temperature MD for a long time; there are papers out there with methodology 
you might be able to follow, but since you have not described your goals (are 
you trying to super-heat a lysozyme solution? improve sampling?) then there is 
nothing specific to offer.

-Justin

> Thank you
> Lin
> 
> 
> 
> 
> 
> I agree with Mark's earlier comment; the water model alone is not the most
> immediate concern.  A colleague of mine is currently doing lots of
> high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER
> force fields.  There are plenty of other methodological concerns (pressure
> coupling especially); a thorough search of the literature will give you some
> insights into what might be wrong.  Plenty of groups have successfully been
> doing high-temperature MD for a number of years.
> 
> -Justin
> 
> Chih-Ying Lin wrote:
>> Hi
>> the water model is TIP3P.
>>
>> Thanks
>> Lin
>>
>>
>>
>> I think the problem is hidden in your water force field model.
>>
>>
>>  > The simulation system is merely water + one lysozyme.
>>  > I increase temperate to 550K.
>>  >
>>  > Then, the simulation broke.
>>  > The following message is shown.
>>  >
>>  > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0)
>>  > mpiexec: Warning: task 0 exited with status 1.
>>  > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed).
>>  > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault).
>>  >
>>  >
>>  > Anything wrong with the simulation?
>>  >
>>  > Thank you
>>

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================